SMTL ID : 6zti.1

Phospholipase PlaB from Legionella pneumophila in complex with thio-NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-tetramer

Ligands

8 x SND: THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

SND.1: 22 residues within 4Å: Chain A: Q.140, L.141, R.145, V.208, N.209, S.210, Y.211, D.380, R.381, Q.382 Chain C: Y.358, D.359, L.360, Y.361, R.381, Q.382, R.383, R.388, L.391, Y.393 Ligands: SND.2, SND.8 19 PLIP interactions: 8 interactions with chain A, 11 interactions with chain C Hydrogen bonds: A:R.145, A:N.209, A:R.381, A:Q.382, C:L.360, C:L.360, C:R.381 Water bridges: A:N.209, A:S.210, C:R.381, C:R.381, C:R.381, C:R.381, C:R.383, C:R.383 Salt bridges: A:R.145, C:R.381, C:R.381 pi-Stacking: A:Y.211 SND.2: 26 residues within 4Å: Chain A: I.200, R.202, Y.205, A.207, V.208, N.209, S.210, G.213, R.333, Y.335 Chain C: L.360, Y.361, L.362, T.363, E.370, Q.371, A.372, L.373, P.374, A.375, G.376, F.377, F.378, R.381, Y.393 Ligands: SND.1 19 PLIP interactions: 10 interactions with chain A, 9 interactions with chain C Hydrogen bonds: A:R.202, A:Y.205, A:Y.205, A:A.207, A:S.210, C:L.362, C:L.362, C:E.370, C:L.373, C:G.376, C:R.381, C:Y.393 Water bridges: A:S.210, A:S.210, A:R.333, A:Y.335, C:R.381 pi-Stacking: A:Y.205, C:F.377 SND.4: 20 residues within 4Å: Chain B: Q.140, L.141, R.145, V.208, N.209, S.210, Y.211, D.380, R.381, Q.382 Chain D: Y.358, D.359, L.360, Y.361, R.381, R.383, L.391, Y.393 Ligands: SND.5, SND.11 18 PLIP interactions: 10 interactions with chain D, 8 interactions with chain B Hydrogen bonds: D:L.360, D:L.360, D:R.381, B:R.145, B:N.209, B:R.381, B:Q.382 Water bridges: D:D.359, D:R.381, D:R.381, D:R.381, D:R.383, B:S.210, B:R.381 Salt bridges: D:R.381, D:R.381, B:R.145 pi-Stacking: B:Y.211 SND.5: 25 residues within 4Å: Chain B: I.200, R.202, Y.205, A.207, V.208, N.209, S.210, G.213, R.333, Y.335 Chain D: L.360, Y.361, L.362, E.370, Q.371, A.372, L.373, P.374, A.375, G.376, F.377, F.378, R.381, Y.393 Ligands: SND.4 16 PLIP interactions: 7 interactions with chain B, 9 interactions with chain D Hydrogen bonds: B:R.202, B:Y.205, B:A.207, B:S.210, D:L.362, D:L.362, D:E.370, D:L.373, D:G.376, D:R.381, D:Y.393 Water bridges: B:R.333, B:Y.335, D:R.381 pi-Stacking: B:Y.205, D:F.377 SND.6: 26 residues within 4Å: Chain B: L.360, Y.361, L.362, T.363, E.370, Q.371, A.372, L.373, P.374, A.375, G.376, F.377, F.378, R.381, Y.393 Chain D: I.200, R.202, Y.205, A.207, V.208, N.209, S.210, G.213, R.333, Y.335 Ligands: SND.11 18 PLIP interactions: 8 interactions with chain B, 10 interactions with chain D Hydrogen bonds: B:L.362, B:L.362, B:E.370, B:L.373, B:G.376, B:R.381, B:Y.393, D:R.202, D:Y.205, D:Y.205, D:A.207, D:S.210 pi-Stacking: B:F.377, D:Y.205 Hydrophobic interactions: D:Y.205 Water bridges: D:S.210, D:R.333, D:Y.335 SND.8: 21 residues within 4Å: Chain A: Y.358, D.359, L.360, Y.361, R.381, Q.382, R.383, L.391, Y.393 Chain C: Q.140, L.141, R.145, V.208, N.209, S.210, Y.211, D.380, R.381, Q.382 Ligands: SND.1, SND.9 17 PLIP interactions: 7 interactions with chain A, 10 interactions with chain C Hydrogen bonds: A:L.360, A:L.360, A:R.381, C:R.145, C:N.209, C:R.381, C:Q.382 Water bridges: A:R.381, A:R.383, C:R.145, C:S.210, C:D.380, C:R.381 Salt bridges: A:R.381, A:R.381, C:R.145 pi-Stacking: C:Y.211 SND.9: 26 residues within 4Å: Chain A: L.360, Y.361, L.362, T.363, E.370, Q.371, A.372, L.373, P.374, A.375, G.376, F.377, F.378, R.381, Y.393 Chain C: I.200, R.202, Y.205, A.207, V.208, N.209, S.210, G.213, R.333, Y.335 Ligands: SND.8 16 PLIP interactions: 9 interactions with chain A, 7 interactions with chain C Hydrogen bonds: A:L.362, A:L.362, A:E.370, A:L.373, A:G.376, A:R.381, A:Y.393, C:R.202, C:Y.205, C:Y.205, C:A.207, C:S.210 Water bridges: A:R.381, C:R.333 pi-Stacking: A:F.377, C:Y.205 SND.11: 20 residues within 4Å: Chain B: Y.358, D.359, L.360, Y.361, R.381, R.383, L.391, Y.393 Chain D: Q.140, L.141, R.145, V.208, N.209, S.210, Y.211, D.380, R.381, Q.382 Ligands: SND.4, SND.6 19 PLIP interactions: 8 interactions with chain B, 11 interactions with chain D Hydrogen bonds: B:L.360, B:L.360, B:R.381, D:R.145, D:N.209, D:R.381, D:Q.382 Water bridges: B:R.381, B:R.381, B:R.383, D:R.145, D:R.145, D:N.209, D:S.210, D:D.380 Salt bridges: B:R.381, B:R.381, D:R.145 pi-Stacking: D:Y.211

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: V.26, T.31, H.99, S.267, G.268, R.275 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.31, A:T.31, A:G.268, A:R.275 Water bridges: A:H.28 GOL.7: 6 residues within 4Å: Chain B: V.26, T.31, H.99, S.267, G.268, R.275 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.31, B:S.267, B:G.268 Water bridges: B:T.31, B:R.275 GOL.10: 6 residues within 4Å: Chain C: V.26, T.31, H.99, S.267, G.268, R.275 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.31, C:T.31, C:R.275 Water bridges: C:K.269 GOL.12: 6 residues within 4Å: Chain D: V.26, T.31, H.99, S.267, G.268, R.275 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.31, D:G.268, D:R.275 Water bridges: D:T.31, D:R.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diwo, M. et al., NAD(H)-mediated tetramerization controls the activity of Legionella pneumophila phospholipase PlaB. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-06-02

Peptides

PlaB phospholipase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PlaB phospholipase

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